The transit agency — which constantly socks riders with fare hikes, the latest coming in March — handed four MTA execs checks totalling $253,000 right before Joe Lhota left the agency to run for mayor.

The checks were cut in December. Lhota’s last day on the job was Dec. 31.

The execs include Metro-North boss Howard Permut, Michael Horodniceanu, the head of mega-projects like Second Avenue Subway, LIRR head Helena Williams, and MTA Bus President Joseph Smith.

Permut, who earns $243,000 a year, received a $98,000 check; Horodniceanu makes $262,000 a year and saw a $61,247 lump-sum check; Williams makes $243,000 and took home a check for $56,000; and Smith was cut a check for $38,000 which included money for deferred raises, as well as unusued vacation and sick time.

Lhota said he was honoring contracts that all three had signed between four and five years ago that called for raises between 3 and 6 percent.

The execs had agreed to forgo the raises for a few years at the request of past MTA chiefs. They weren’t willing to continue the practice and at least one was threatening to sue, sources told the Post.

“A contract is a contract is a contract. It’s as simple as that,” Lhota told the Post. “I inherited those contracts. They were never declining raises, they were only deferring them.”

Lhota said he refused to pay interest on the deferred payments, but agreed to cut the checks for what they were owed after consulting attorneys.

The deferments began under former MTA chief Elliot Sander in 2009 as the agency was begging the Legislature for a bailout to help it close its budget gap and avoid service cuts.

“The MTA is keeping its word,” MTA spokesman Adam Lisberg said. “They were asked not accept the raises at the time but not to permanently forgo them.”

MTA managers are now in their fourth year without a raise, while their unionized underlings have gotten annual bumps for the past three years.

In 2011, the Transport Workers Union snagged a 3 percent pay hike for its workers on top of 2.5 percent pay hikes in 2009 and 2010.